Man pages for BIGDAWG
Case-Control Analysis of Multi-Allelic Loci

AAmino Acid Analysis Function
AA.df.checkContingency Table Check
AAtable.builderAmino Acid Contingency Table Build
AlignmentFilterAlignment Filter
AlignObj.CreateAlignment Object Creator
AlignObj.UpdateUpdated Alignment Object Creator
Append.SystemAppend Genetic System Locus Designation to Allele String
A.wrapperAmino Acid Wrapper
BIGDAWGBIGDAWG Main Wrapper Function
buildHAPnamesHaplotype Name Builder
buildHAPsetsHaplotype List Builder
Build.MatrixBuild Output Matrix for GL2Tab Conversion
cciCase-Control Odds ratio calculation and graphing
cci.pvalCase Control Odds Ratio Calculation from Epicalc
cci.pval.listCase Control Odds Ratio Calculation from Epicalc list...
CheckAllelesHLA Allele Legitimacy Check for Amino Acid Analysis
Check.CoresCheck Cores Parameters
Check.DataCheck Data Structure
CheckHLAHLA Formatting Check for Amino Acid Analysis
CheckLociHLA Loci Legitimacy Check for Amino Acid Analysis
Check.ParamsCheck Input Parameters
Check.Params.GLSCheck Input Parameters for GLS conversion
CheckReleaseFunction to Check Release Versions
CheckString.AlleleGL String Allele Check
CheckString.LocusGL String Locus Check
Create.Null.TableCreate Empty Table
DRB345.Check.WrapperDRB345 haplotype zygosity wrapper
DRB345.Check.ZygosityDRB345 haplotype zygosity checker single locus
DRB345.ExpDRB345 Expected
DRB345.parserDRB345 Column Processing
Err.LogError Code Display and Logging
EVSremovalExpression Variant Suffix Removal
ExonPtnAlign.CreateProtein Exon Alignment Formatter
ExonPtnListExon 2 (class II) or 2/3 (class I) protein alignments.
FillerReplace or Fill 00:00 allele strings
Format.AlleleAmbiguous Alleles Locus Name Formatting
Format.TabTabular Data Locus Format Tool
getAllele.CountRecompute number of alleles
getCS.MatChi square matrices
getCS.statChi square test statistic
GetFieldHLA trimming function
getFileNameFile Name Extraction
GetFilesFile Fetcher
getHapHaplotype Table Maker
getObsFreqObserved Frequency
GL2Tab.LociLocus Ordering for GL2Tab
GL2Tab.SubGenotype List String Expander
GL2Tab.wrapperGenotype List String to Tabular Data Conversion
GLSconvertGenotype List String Conversion
HLA_dataExample HLA Dataset
H.MCHaplotype Analysis Function for Multicore
H.MC.wrapperHaplotype Wrapper for Multicore
HWEHardy Weinbergy Equilibrium Function
HWE.ChiSqHardy Weinbergy Equilibrium Function
HWE.wrapperHardy-Weinbery Wrapper
LLocus Analysis Function
L.wrapperLocus Wrapper
make2x2Creation of a 2x2 table using the indicated orientation.
makeCombGenotype Combination Maker
MergeData_OutputData Object Merge and Output
PgrpExtractHLA P group Finder
PgrpFormatHLA P group File Formatter
PreCheckData Summary Function
prepDataPrepare imported data
rmABstringsReplace absent allele strings
RunChiSqChi-squared Contingency Table Test
StripperRemoves System and Locus from Alleles
summaryGeno.2Haplotype missing Allele summary function
Tab2GL.LociLocus Condenser for Tab2GL
Tab2GL.SubGenotype List String Condenser
Tab2GL.wrapperGenotype List String to Tabular Data Conversion
TableMakerTable Maker
UpdateReleaseUpdate function for protein aligment upon new IMGT HLA data...
BIGDAWG documentation built on Feb. 9, 2018, 6:08 a.m.